Onions do not like a lot of nitrogen in the soil, and recently added manure also increases the risk of rotting, so its always best to add composted manure six months before you want to plant. They also don't like heavy, wet soil, preferring free draining planting conditions, and they don't like a soil ph below 6.5. Not sure what the ph value of your cow manure would have been, it shouldn't really have made the soil more acidic, so that probably isn't the issue.
It might just be that they're in a heavy soil, and there's too much nitrogen available - poor drainage in heavy soils also greatly increases the risks of fungal infection and rotting, and causes poor growth.